Table 3.

Epigenetic changes during each phase of memory

Memory Phase	Mechanism	Structure	Modification	Effect	Timepoint	Type of FC	Citation
Consolidation	HAT	Amygdala	H3 acetylation	Increased	90m post-ACQ (not 30 or 60m)	Auditory	[34, 44, 45]
			HAT activity	Increased	10m to 6h post-ACQ	Auditory	[46]
		Hippocampus	H3 acetylation	Increased	1h post-ACQ	Context	[35, 40, 47, 48]
			H3 acetylation at Homer1 promoter	Increased	2h post-ACQ	Auditory	[41]
			H3 acetylation & phosphoacetylation	Increased	2h post-ACQ	Context	[49]
	DNMT	Amygdala	DNMT3A protein expression	Increased	90m post-ACQ (not 30 or 60m)	Auditory	[44]
		Hippocampus	Methylation of Bdnf promoter exon VI	Increased	2h post-ACQ	Context	[49]
			Methylation of Bdnf promoter I & IV	Decreased	2h post-ACQ	Context	[49]
			DNMT3A & 3B mRNA expression	Increased	30m post-ACQ	Context	[31]
			PP1 methylation	Increased	1h (but not 24h) post-ACQ	Context	[31]
			Reln methylation	Decreased	1h (but not 24h) post-ACQ	Context	[31]
		mPFC	Reln methylation	Increased	1h post-ACQ	Context	[64]
			Zif268 methylation	Decreased	1h post-ACQ	Context	[64]
	HPO4	Hippocampus	H3 phosphorylation	Increased	1h post-ACQ	Auditory	[35]
			H3 phosphorylation & acetylation	Increased	1h post-ACQ	Context	[48]
	HKM	Amygdala	H3K9me at Homer1 promoter	Decreased	2h post-ACQ	Auditory	[41]
		Hippocampus	H3K4me3	Increased	1h (but not 24h) post-ACQ	Context	[39, 52]
			H3K4me3 at Bdnf promoter 1	Increased	30m post-ACQ	Context	[39]
			H3K4me3 at Zif268 promoter	Increased	30m post-ACQ	Context	[39]
			H3K9me2	Increased	1h post-ACQ	Context	[39]
			H3K9me2 at Comt promoter	Increased	1h post-ACQ	Context	[52]
			H3K9me2 at Zif268, cFos, BDNF IV promoters	Decreased	1h post-ACQ	Context	[52]
		Entorhinal Ctx	H3K4me3	Increased	1h post-ACQ	Context	[52]
			H3K9me2 at cFos, BDNF IV promoters	Increased	1h post-ACQ	Context	[52]
			H3K9me2	Increased	1h (but not 24h) post-ACQ	Context	[52]
Storage	HAT	mPFC	H3 acetylation at Bdnf promoter 1&4	Increased	1d post-ACQ (2h after novel context	Auditory	[88]
	DNMT	dmPFC	Reln methylation	Increased	1d & 7d (but not 30d) post-ACQ	Context	[64]
			Z if 268 methylation	Decreased	1d, 7d, 30d post-ACQ	Context	[64]
			CaN methylation	Increased	1d, 7d, 30d post-ACQ	Context	[64]
	HKM	Hippocampus	H3K9me2	Decreased	1d post-ACQ	Context	[39, 52]
		Entorhinal Ctx	H3K4me3	Decreased	1d post-ACQ	Context	[52]
Reconsolidation	HAT	Amygdala	H3 acetylation	Increased	90m (not 60m or 120m) post-retrieval	Auditory	[34, 45, 78]
		Hippocampus	HDAC2 bound to cFos promoter	Decreased	1h post-retrieval of recent memory	Context	[77]
			H3 phosphorylation and acetylation	Increased	1h post-retrieval	Context	[76]
			H3 phosphoacetylation and acetylation at Zif268	Increased	1h post-retrieval	Context	[76]
			H3 phosphorylation and acetylation at IKBα	Increased	1h post-retrieval	Context	[76]
			AcH3K9/14 binding to cFos promoter	Decreased	1h post-retrieval of remote memory	Context	[77]
Extinction	HAT	Hippocampus	H3K9 acetylation at cFos promoter	Decreased	1h post-EXT	Context	[92]
			HDAC1 binding at cFos promoter	Increased	1h post-EXT	Context	[92]
		IL mPFC	CBP expression	Decreased	2h post-EXT	Auditory	[91]
		mPFC	p300 expression	Decreased	2h post-EXT	Auditory	[91]
			PCAF expression	Increased	2h post-EXT	Auditory	[91]
			HDAC2 expression	Decreased	2h post-EXT	Auditory	[91]
			H3 acetylation at Bdnf promoter 1	Decreased	2h post-EXT	Auditory	[88]
			H3 acetylation at Bdnf promoter 4	Increased	2h post-EXT	Auditory	[88]
			H4 acetylation at Bdnf promoter 4	Increased	2h post-EXT	Auditory	[88]
	DNMT	IL mPFC	MECP2 expression	Increased	2h post-EXT	Auditory	[91]
			H3R2Me2s	Increased	2h post-EXT	Auditory	[93]
	HKM	Hippocampus	H3K9me3 at cFos promoter	Increased	1h post-EXT	Context	[92]
		IL mPFC	H3K9me2 expression	Decreased	2h post-EXT	Auditory	[91]

Abbreviations: ACQ: Acquisition; Ctx: Context; DNMT: DNA methyltransferase or methylation-related process; EXT: Extinction; HAT: Histone acetyltransferase; HKM: Histone lysine methylation; HPO₄: histone phosphorylation; mPFC: Medial prefrontal cortex; dmPFC: dorsomedial prefrontal cortex; IL: infralimbic